Do you have your joystick mounted to the top of the board or the underside of it? I mounted mine to the top, and the only way to countersink the screws would be to shave off some joystick plastic. So I'm going to just have screwheads showing.
(or I could drill little holes in the Lucite where the screws are, and they'd be recessed that way, but I dunno if I wanna do that.)
Don't screw your joy stick until the hole fits!!!
(sorry I couldn't resist)